A custom server, as in, having a dedicated copy of the Wiimmfi server run just for your game, is not possible. But it's also not needed - there's other ways to filter which players you can connect to.

For example, in Mario Kart Wii there's continental matches where the game requests from the server "Hey Wiimmfi, let me find some other players that are also in region 2" (for example). Nintendo only ever used region numbers 0 to 9, so all the numbers higher than that are custom regions used to distinguish different mods and filter matchmaking.

Question is, what's the best way to implement this in another game. I checked Dragon Ball's matchmaking table on Wiimmfi and it doesn't seem to have a similar convenient region mechanism that could be used.

Does the game use global, non-friend matchmaking (like MKWii's global or continental matches) or friend matchmaking (like MKWii's friend rooms)? Or both?

For friend rooms you could do what CTGP does, and inject some own code into the STATUS message handlers to communicate with other players that they need a certain version of your mod installed to join a particular friend room. But that solution isn't ideal for worldwide matches due to how matchmaking works.

What do you mean it uses its own friendcode system? I'm not aware of any game doing that.

Or do you mean the friend codes displayed on the Wiimmfi site are wrong and don't match the one displayed in-game, but they still have the same format? (xxxx-xxxx-xxxx or xxxxxx-xxxxxx)

That's usually a simple fix, all we need for that is your friend code as displayed on Wiimmfi and your friend code as displayed in-game, and we can correct that for all players of that game.

Your friend code is the NDS encoding of the PID:

Is that friend code discrepancy something that just happens with your mod, or does this happen with the base game as well? If it happens with the base game as well we can fix that fairly easily on the Wiimmfi server for everyone.

Then that's something we can easily fix on the Wiimmfi server, when Wiimm updates the game database the next time this error should be gone.

I don't think changing the gameID is a good idea, these are fairly limited and the ID4 isn't really a good indicator to differentiate between mods.

I assume that with all the code changes you did to the game already, you probably have some framework to inject C code into the game? Or is this all gecko codes and file edits? If you can inject custom code you could just add a couple custom login parameters to signal to Wiimmfi that you want your own dedicated region. Though that would require some work on Wiimmfi to get that to work and I'm not sure when we'll have time to implement that.